At its most basic level, the ship is run by the Palatine, a clan of indentured servants in all-encompassing grey robes and masks, who act as intermediaries between the Holders of the Warrant and the Crew Clans. The Clan Chieftains of the various extended families that make up the Crew Clans also hold a certain amount of power, predominately over the areas for which they are responsible, and expect their advice to be taken into account by those in command of the ship. The entire crew, from the lowliest deck-scrubber to the highest chieftain, views Absolon Van Daark as the Ship Father and the symbolic head of their family. As the Chosen of the Ship Father, Theophilius, Kateryna, Charlie, Kerghan and Vyn are also accorded honour. The missionary Herman Malvert was not initially given anywhere near this level of respect, but his services to the crew, heroism and miraculous healing powers have given him an edge.

In addition to a labyrinthine system of holds and hidden storage rooms, the ship has also been outfitted with a full complement of murder servitors. While there has been much speculation of their original purpose, they have so far been used by the current team only once; when the Warp affected several members of the crew.

The Vulpis Nigerei has room to carry a small number of atmospheric and void capable transport craft in its hanger deck.